Fig. 1. Expression array analysis of E13.5 trigeminal ganglia. (A) A two-dimensional plot of the hybridization signal for 4,000 present transcripts, including ESTs, in one of the two experiments comparing Brn3a heterozygous and knockout trigeminal ganglia. Values for the expression of the majority of transcripts fall along the central diagonal line representing equal expression in the two genotypes. A few transcripts fall outside the parallel lines indicating a greater than twofold change in expression, and examples of some highly changed transcripts are indicated. (B) To determine whether Brn3a heterozygosity results in intermediate levels of target gene expression, two-way comparisons were made between transcript levels in knockout versus wild-type, knockout versus heterozygous and wild-type versus heterozygous ganglia for the 41 increased and 62 decreased transcripts from the U74Av2 array, Experiment 1. Expression levels in wild type and heterozygotes showed a similar mean fold increase or decrease when compared to those in the knockout. However, comparison of expression levels in heterozygotes with those in wild type revealed no significant difference (fold change 1, red horizontal line) for either the increased or decreased transcripts. As expected, the fold change was also approximately 1 for two-way comparisons between the genotypes for a group of 160 unchanged neural transcripts (0.003<change-p<0.997; see Supplemental Data, http://dev.biologists.org/supplemental/).